grinch | global report investigating novel coronavirus haplotypes

New variant report 2020-12-27



Data source and processing

All whole genome SARS-CoV-2 sequences were pulled from GISAID at 2020-12-27 12:19 GMT. The genomes were de-duplicated based on GISAID sequence name – note that the publically available metadata may not fully allow us to de-duplicate by patient. Full data processing pipeline found here.

The sequences were then assigned lineages with pangolin v2.1.3, pangoLEARN version 2020-12-17.

Pangolin assigns B.1.1.7 to sequences with more than 4 of the 17 defining B.1.1.7 SNPs (defined here and B.1.351 to any sequences with more than 3 of the 5 defining B.1.351 SNPs.

Table 1 | Summary of data

Lineage Country Sequence count Earliest sequence Travel history
B.1.351 South_Africa 259, UK 1 260 2020-10-08
B.1.1.7 UK 4249, Italy 11, Denmark 9, Ireland 7, Netherlands 3, Australia 3, Hong_Kong 2, Singapore 1, Israel 1, France 1 4287 2020-09-20

Lineage B.1.351

Caveat: Most locations outside the original focus have not reported sustained transmission and many cases have known travel links to the focal location. Increasing numbers of international cases is currently likely due to increased surveillance and vigilance.

Table B.1.351 | Lineage B.1.351

Statistic Information
Count 260
Likely origin South Africa
SNPs aa:orf1ab:K1655N
aa:S:D215G
aa:S:E484K
aa:S:N501Y
snp:C23664T

Figure 1 | Cumulative sequence count over time B.1.351

2020-12-27T16:30:00.834962 image/svg+xml Matplotlib v3.3.3, https://matplotlib.org/

Figure 2 | Date of earliest B.1.351 detected

2020-12-27T16:30:00.374708 image/svg+xml Matplotlib v3.3.3, https://matplotlib.org/

Figure 3 | Map of B.1.351 sequence counts

2020-12-27T16:30:00.603416 image/svg+xml Matplotlib v3.3.3, https://matplotlib.org/

Figure 4 | Sequence count per country B.1.351

2020-12-27T16:30:00.737129 image/svg+xml Matplotlib v3.3.3, https://matplotlib.org/

Figure 5 | Frequency B.1.351 in sequences produced since first new variant reported per country

2020-12-27T16:30:00.925916 image/svg+xml Matplotlib v3.3.3, https://matplotlib.org/

Lineage B.1.1.7

Caveat: Most locations outside the original focus have not reported sustained transmission and many cases have known travel links to the focal location. Increasing numbers of international cases is currently likely due to increased surveillance and vigilance.

Table B.1.1.7 | Lineage B.1.1.7

Statistic Information
Count 4287
Likely origin United Kingdom
SNPs aa:orf1ab:T1001I
aa:orf1ab:A1708D
aa:orf1ab:I2230T
del:11288:9
del:21765:6
del:21991:3
aa:S:N501Y
aa:S:A570D
aa:S:P681H
aa:S:T716I
aa:S:S982A
aa:S:D1118H
aa:Orf8:Q27*
aa:Orf8:R52I
aa:Orf8:Y73C
aa:N:D3L
aa:N:S235F

Figure 6 | Cumulative sequence count over time B.1.1.7

2020-12-27T16:29:57.242853 image/svg+xml Matplotlib v3.3.3, https://matplotlib.org/

Figure 7 | Date of earliest B.1.1.7 detected

2020-12-27T16:29:56.675646 image/svg+xml Matplotlib v3.3.3, https://matplotlib.org/

Figure 8 | Map of B.1.1.7 sequence counts

2020-12-27T16:29:56.959385 image/svg+xml Matplotlib v3.3.3, https://matplotlib.org/

Figure 9 | Sequence count per country B.1.1.7

2020-12-27T16:29:57.119014 image/svg+xml Matplotlib v3.3.3, https://matplotlib.org/

Figure 10 | Frequency B.1.1.7 in sequences produced since first new variant reported per country

2020-12-27T16:29:57.366655 image/svg+xml Matplotlib v3.3.3, https://matplotlib.org/

Figure 11 | Air traffic from UK by destination

The number of ticketed origin-to-destination journeys from London airports to countries outside the United Kingdom during October 2020.

Colours indicate numbers of published genomes of B.1.1.7 deposited on GISAID as of December 26, 2020. Grey bars indicate countries that have reported the presence of the variant but have not yet published B.1.1.7 sequences on GISAID as of the 26-Dec-2020. White bars indicate countries with no reports of B.1.1.7.

Flight data come from the International Air Transportation Association that capture anonymized, passenger-level flight itinerary data, comprising both commercial flights and scheduled charter flights. These data account for ~90% of global air travel volumes, with the remaining volumes modelled using market intelligence. We report data from destinations including >5,000 passengers.

Figure by Kamran Khan, Isaac Bogoch, Alexander Watts, Oliver Pybus, Moritz Kraemer

Flights from UK